GitHub - gzluo/NGS: Scripts for next generation sequencing

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Scripts for next generation sequencing

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Name		Name	Last commit message	Last commit date
Latest commit History 187 Commits
trash		trash
.overlappedRegionsAmongMultipleSamples.py.swp		.overlappedRegionsAmongMultipleSamples.py.swp
affy_deGenes.sh		affy_deGenes.sh
affy_full.sh		affy_full.sh
asType.py		asType.py
bdgToWig.py		bdgToWig.py
bed12Tobed6.py		bed12Tobed6.py
bedCovrageUseWig.py		bedCovrageUseWig.py
bedCovrageUseWig.readBedIn.py		bedCovrageUseWig.readBedIn.py
bedToWig.py		bedToWig.py
bedgraphToWig.py		bedgraphToWig.py
binRegionForCovRpkm.py		binRegionForCovRpkm.py
binRegions.py		binRegions.py
binTranscriptome.py		binTranscriptome.py
binmRNARegions.py		binmRNARegions.py
bowtiemap.sh		bowtiemap.sh
bwamap.sh		bwamap.sh
ceasDumpClassify.py		ceasDumpClassify.py
cellnet.sh		cellnet.sh
clipAdaptor.py		clipAdaptor.py
coLinearAnalysisForFindMotifResult.py		coLinearAnalysisForFindMotifResult.py
collapseBySTring.py		collapseBySTring.py
collapsemiRNAreads.py		collapsemiRNAreads.py
correCoefficientMatrix.sh		correCoefficientMatrix.sh
countReadsOfSamPE.py		countReadsOfSamPE.py
cpgCountPercent.py		cpgCountPercent.py
cuffdiff.systemtial_DE.py		cuffdiff.systemtial_DE.py
cuffdiff.transfer_diff.py		cuffdiff.transfer_diff.py
deGene_norepeat.py		deGene_norepeat.py
deGene_withRepeat.sh		deGene_withRepeat.sh
deleteNinFASTQ.py		deleteNinFASTQ.py
deleteOverlap_assist_getSingleTranscriptSet.py		deleteOverlap_assist_getSingleTranscriptSet.py
determineCentralMismatchForMiRNAs.py		determineCentralMismatchForMiRNAs.py
determineThePosOfPeakFromIntersectBedOutput.py		determineThePosOfPeakFromIntersectBedOutput.py
extendReadsToCertainLength.py		extendReadsToCertainLength.py
extendReadsinBam.py		extendReadsinBam.py
extractFastqByName.py		extractFastqByName.py
formatFasta.py		formatFasta.py
geneAnnoBedToNormalBed.py		geneAnnoBedToNormalBed.py
geneSetByLen.py		geneSetByLen.py
geneSetByVal.py		geneSetByVal.py
generateRandomSeq.py		generateRandomSeq.py
genomeStructure.py		genomeStructure.py
getExonIntronBoundaryAndTypeFromBed-GTF.py		getExonIntronBoundaryAndTypeFromBed-GTF.py
getFirstNtOftranscriptsAndFlankStopCodon.py		getFirstNtOftranscriptsAndFlankStopCodon.py
getFirstNtOftranscriptsAndFlankStopCodon.py.bak		getFirstNtOftranscriptsAndFlankStopCodon.py.bak
getHairpin.py		getHairpin.py
getHalfExon.py		getHalfExon.py
getJuncsFromBed.py		getJuncsFromBed.py
getRandomLinesFromFile.py		getRandomLinesFromFile.py
getSeqOfLocus.py		getSeqOfLocus.py
getSingleTranscriptSet.py		getSingleTranscriptSet.py
getUnionedExon.py		getUnionedExon.py
hcp_icp_lcp.py		hcp_icp_lcp.py
kmeans.test.sh		kmeans.test.sh
localLambdaScore.py		localLambdaScore.py
locatemRNAFragToGenome-parralize.py		locatemRNAFragToGenome-parralize.py
locatemRNAFragToGenome.py		locatemRNAFragToGenome.py
locatemRNAToGenomeUsingBlat.py		locatemRNAToGenomeUsingBlat.py
mergeBed.nms.peak_overlap_status.py		mergeBed.nms.peak_overlap_status.py
mergeBed.py		mergeBed.py
mergeCeasForGeneProfile.py		mergeCeasForGeneProfile.py
mergeDuplicateGenesForExpressionMatrix.py		mergeDuplicateGenesForExpressionMatrix.py
mergeWigFiles.py		mergeWigFiles.py
mirBaseGetInfo.py		mirBaseGetInfo.py
nat_summarizeCis-nat.py		nat_summarizeCis-nat.py
normPeak.py		normPeak.py
normalizeMatrix.sh		normalizeMatrix.sh
oligo_full.sh		oligo_full.sh
oneToOthersCompare.py		oneToOthersCompare.py
overlappedRegionsAmongMultipleSamples.py		overlappedRegionsAmongMultipleSamples.py
parseBwaNohup.py		parseBwaNohup.py
parseCuffDiff.2.sh		parseCuffDiff.2.sh
parseCuffDiff.py		parseCuffDiff.py
parseCuffDiff.sh		parseCuffDiff.sh
parseCuffcompare_Tmap.py		parseCuffcompare_Tmap.py
parseCuffmerge.merged_gtf.py		parseCuffmerge.merged_gtf.py
parseGTF.2.py		parseGTF.2.py
parseGTF.bak.py		parseGTF.bak.py
parseGTF.py		parseGTF.py
parseMirandaOutput.py		parseMirandaOutput.py
parseRNAfoldOutput.py		parseRNAfoldOutput.py
parseRpeatRandomMOtifCompare.py		parseRpeatRandomMOtifCompare.py
parsemirBase.dat.embl.py		parsemirBase.dat.embl.py
parserelativePositonOfMultipleSites.py		parserelativePositonOfMultipleSites.py
pasteFiles.py		pasteFiles.py
pasteMultipleFiles.py		pasteMultipleFiles.py
pasteMultipleFilesSpecialCol.py		pasteMultipleFilesSpecialCol.py
pickNamesofUnmappedReads.py		pickNamesofUnmappedReads.py
profileCeasR.py		profileCeasR.py
proteinCorrelation.blast.sh		proteinCorrelation.blast.sh
pythonmail3.py		pythonmail3.py
quantifier.modified.pl		quantifier.modified.pl
quantifier.sh		quantifier.sh
randomPos.py		randomPos.py
relativePositonOfMultipleSites.py		relativePositonOfMultipleSites.py
removeDuplicateGenesForExpressionMatrix.py		removeDuplicateGenesForExpressionMatrix.py
reorderFasta.py		reorderFasta.py
rmMultipleMatchedTrimmedReads.py		rmMultipleMatchedTrimmedReads.py
samToWig.py		samToWig.py

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Scripts for next generation sequencing

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